hap.py
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Illumina
Haplotype VCF comparison tools
Hi, I have installed hap.py as instructed and running on the example data set. it gives me below error python ~/softwares/hap.py-build/bin/som.py /uufs/chpc.utah.edu/common/home/u0944235/SPIKEinData/ClinVarInjection/BamBlasterFinal/clinvarToInjectB37_edited_included.vcf.gz ../0.001Var_Consensus.all.vcf.gz -f ~/BioApps2/HunterKeith/HSV1_GBM_IDT_Probes_B37Pad25bps.bed -o test File "/uufs/chpc.utah.edu/common/home/u0944235/softwares/hap.py-build/bin/som.py", line...
If I run this command hap.py-build/bin/hap.py Platinum_genome/split/chr1.recode.vcf 11_Haplotypecaller_indelrealigner/SRR622457_chr1.vcf -f 11_gatk_targetrealign/Chr1_SRR622457.bed -r /root/Work/ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa --scratch-prefix Temp/ -o test 2019-02-11 14:08:50,974 WARNING No reference file found at default locations. You can set the...
log: ``` 2018-02-14 09:30:18,372 ERROR Command 'quantify /tmp/hap.py.result.jryogM.vcf.gz -o /mnt/yard2/ian/structural_variants/CHM1_CHM13_analysis/HG2.happy.roc.tsv -r /mnt/opt/refdata_new/hg19-2.0.0/fasta/genome.fa --threads 8 --output-vtc 0 --output-rocs 1 --type xcmp --qq IQQ --qq-header QUAL --roc-delta 0.500000 --clean-info 1 --fix-chr-regions 0...
When using the -R option to restrict the analysis to a region of interest, we noticed that variants in the query are only evaluated if they are on a chromosome...
I have two VCF files, A and B. A contains this variant, whereas B does not: 1 13133936 . G A 286.80 VQSRTrancheSNP99.90to100.00 AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=26.00;SOR=1.609;VQSLOD=-3.650e+01;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,7:7:21:1|1:13133936_G_A:315,21,0 When I run hap.py...
Cmake does not respect non-system default compilers using the conventional override methods (CC env variable and PATH). https://stackoverflow.com/questions/29902862/how-to-get-cmake-to-use-the-default-compiler-on-system-path
Hello, This is not an issue, but a request/suggestion for python3 support. Looks like the installation of Hap.py require python2 and python2 packages so just wondering if there will be...
Hi, I made an attempt to install. CentOS 7.5, version master (git checkout) : ``` cmake ../hap.py \ -DCMAKE_C_COMPILER=/config/binaries/gcc/8.2/bin/gcc \ -DCMAKE_CXX_COMPILER=/config/binaries/gcc/8.2/bin/g++ \ -DCMAKE_BUILD_TYPE=Release \ -DBOOST_ROOT=/config/binaries/boost/1.68.0 ``` But it failed at...
Hi, Thank you for this great tool. i'm curious as to how the QQ field is calculated when --roc DP flag is used Here is an example output vcf:. in...
NA12878 reads (coverage approx. 42x) mapped using bwa-0.7.15. Variant calling using Strelka2 2.9.9. Then, hap.py 0.3.10 fails with message: [W] overlapping records at chr1:37070742 for sample 0 [W] Variants that...
